Thanks for your post. This same question was actually asked back in 2005 (ref. SC-1308) and the request was closed, with a comment of:

No plans to do this

While indeed it would be more efficient from SQL Server's point of view, because of sp_rename it would confuse system tables, and it would NOT be more efficient in SQL Compare (indeed it would be much more inefficient)

I'm not sure of any more detailed reason as to why it would be more inefficient in SQL Compare unfortunately as that's all that was written on the request, but it sounds like performing the rename could actually make the problem worse and we have no plans to fix it.